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Dev #54

Merged
merged 119 commits into from
Sep 30, 2023
Merged

Dev #54

merged 119 commits into from
Sep 30, 2023

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MarieLataretu
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MarieLataretu and others added 30 commits June 24, 2021 16:10
@MarieLataretu
removed unused output
a06a086
@MarieLataretu
test teloclip, rm code redundancy
eaffc5c
@MarieLataretu
assembly
79ee233
@MarieLataretu
added custom soft-clip filter
2a8b433
@MarieLataretu
added env
de98d8a
@MarieLataretu
added the right env
30d0ab6
@MarieLataretu
switch to https cloning
f0a08c5
@MarieLataretu
added mem
10a044d
@MarieLataretu
other parameter
e5d7125
@MarieLataretu
Merge branch 'MarieLataretu/issue23' of github.com:hoelzer/clean into…
1c9cbd1 
… MarieLataretu/issue23
@MarieLataretu
https and ssh cloning
655cda1
@MarieLataretu
cli param for minClip
7cc48cd
@MarieLataretu
bam also for fasta
8257a16
@MarieLataretu
Merge branch 'master' into dev
d8a3df0
@MarieLataretu
added fastq from bam
513a501
@MarieLataretu
handle also paired-end reads
58f8d3c
@hoelzer
Merge pull request #39 from hoelzer/MarieLataretu/issue23
afd98a2 
Marie lataretu/issue23
@MarieLataretu
reference index file incomplete
919fb86 
Fixes #40
@hoelzer
Merge pull request #41 from hoelzer/MarieLataretu/issue40
5e29c9a 
reference index file incomplete
@MarieLataretu
hotfix minimap2 fasta
b3c5679
@MarieLataretu
rename output,fix multiqc barplot,add ambig stats
6d65177
@MarieLataretu
update also for illumina, rm foo xD
ee9c855
@MarieLataretu
typo
a84efef
@MarieLataretu
first commit
27d8ecd
@MarieLataretu
fixes #42
d559162
@MarieLataretu
Merge pull request #43 from hoelzer/MarieLataretu/issue42
afcb6c2 
Marie lataretu/issue42
@MarieLataretu
added min_clip to help
92a4668
@MarieLataretu
--min_clip, typo
303e8f8
@MarieLataretu
fixed stats for fasta
a9cbdd0
@MarieLataretu
idxstats for fasta
64cb857
@MarieLataretu MarieLataretu marked this pull request as ready for review May 5, 2022 13:41
@MarieLataretu
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MarieLataretu commented May 5, 2022 •
edited
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  • introduces sub workflow
  • different input params with --input '*/*.R{1,2}.fastq' --input (nano|illumina|illumina_single_end|fasta)

fixes & features

@MarieLataretu MarieLataretu requested a review from hoelzer May 5, 2022 14:34
MarieLataretu added 10 commits May 5, 2022 17:10
@MarieLataretu
updated readme
e68cb1d
@MarieLataretu
added missing varable for eno
969d606
@MarieLataretu
remmoved old stats line
95b5ab5
@MarieLataretu
fixed typo
2aa6b81
@MarieLataretu
fix fasta input
425b0bf
@MarieLataretu
added conda profile
8dddbdf 
the old conda profile was actually a mamba profile
@MarieLataretu
publish results in sample specific subdirs
6cc2251 
else it gets quite crowded, when processing multiple samples
@MarieLataretu
publish idxstats
122d25b 
good to have them also published, not only in multiqc
@MarieLataretu
make naming more consistent
5e71943 
replace _ with . in flagstats and idxstats
@MarieLataretu
rename sorted bams
44aeedd 
remove "_sorted" suffix
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hoelzer commented May 29, 2023 •
edited
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I tried

nextflow run clean.nf --input_type nano --input ../15-2067_O09_Nano.fastq.gz --host hsa --control dcs -profile local,docker

which failed bc of

ERROR ~ No such variable: hostNameChannel

 -- Check script './workflows/prepare_contamination_wf.nf' at line: 41 or see '.nextflow.log' file for more details

and I think the channel is missing in the subworkflow. The same for ownFastaChannel. I am fixing this and testing right now and will push my changes here for you to check @MarieLataretu ! Bc/ maybe I get smt wrong of how you implemented everything ;)

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hoelzer commented May 29, 2023

Alright, working on my end.

MarieLataretu and others added 9 commits June 21, 2023 08:55
@MarieLataretu
Update nextflow.config
e67ba01 
- enable conda explicitly
- pipeline reports with timestamp
@MarieLataretu
added citations
215b02a
@MarieLataretu
readme updates
0ed1b52 
- nicer workflow figure
- added preprint
- updated mail and nextflow version
@MarieLataretu
added --cleanup_work_dir
54be3fd 
-  sets the nextflow configuration `cleanup` accordingly
@MarieLataretu
directly compress and publish reads/fastas
2d44899 
solves #58
@MarieLataretu
make cleanup_work_dir a valid parameter
a19b0d9
@MarieLataretu
Merge pull request #59 from hoelzer/feature_clean-work-dir
6bf2364 
Feature clean work dir
@MarieLataretu
added changelog
62d95f5
@MarieLataretu
minor text change
f93b028
@MarieLataretu MarieLataretu merged commit 211fced into master Sep 30, 2023
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@MarieLataretu @hoelzer